R-Toolkit - FreqAllele

An R script for generating allele frequencies from DNA/amino acid sequence alignments.

NB: It's worth noting that the script (inside the 01_R_scripts directory) ignores indels/gaps in the alignment

• Input is an alignment in Phylip format which can be generated in many programs such as Aliview.

• Incase you choose to use Aliview, load your alignmnent and click on:

  • File -> Save as Phylip (full names & padded)

• Point the script to your input file in the 03_data_input directory (line 25).

• Run the entire script and you'll find your output in the 04_data_output directory, which will look like the example below.

• The dominant/major alleles are grouped under major, while minor variants are grouped under minor_1, minor_2, e.t.c.

  • locus - represents the position of the allele in the sequence alignment.
  • major - represents the major allele, followed by relative frequency and the number of sequences harbouring the allele
  • minor - represents the minor allele, followed by relative frequency and the number of sequences harbouring the allele

locus	major	minor_1	minor_2
64	A / 98 [49]	G / 2 [1]
79	A / 97.9 [47]	G / 2.1 [1]
241	A / 98 [50]	T / 2 [1]
448	T / 96 [48]	A / 4 [2]
467	G / 98 [49]	A / 2 [1]
470	A / 82 [41]	G / 18 [9]
502	G / 98.1 [53]	C / 1.9 [1]
515	A / 98.2 [56]	G / 1.8 [1]
592	A / 98.6 [69]	T / 1.4 [1]
593	C / 98.6 [69]	A / 1.4 [1]
676	A / 93.4 [71]	G / 3.9 [3]	R / 2.6 [2]
820	G / 56.2 [45]	A / 40 [32]	R / 3.8 [3]
835	G / 65 [52]	A / 33.8 [27]	R / 1.2 [1]